Whitepapers

Inexact Search Acceleration on FPGAs Using the Burrows-Wheeler Transform

Abstract—Inexact search is a difficult and time-consuming task with widespread application. Acceleration of inexact search could have tremendous impact upon fields such as chemistry, meteorology, and even bioinformatics.Field-programmable gate arrays provide a means by which to accelerate this process. We demonstrate the acceleration of inexact search using the Burrows-Wheeler transform on FPGAs using the short read mapping problem in bioinformatics as an example application. Using twelve FPGAs, we are able to accelerate the search of 100-base short reads against the human genome by 48X.